Congenital hypothyroidism (CH) occurs in 1:4000 live births. Neurological disturbances like speech delay, motor delay and lower IQ were reported in children with CH. Evidence from animal experiments indicate that CH is associated with high frequency of deafness. Morphological changes of the external and internal cholera hairs were reported in mutagenic mice with CH. Anatomical changes of the internal ear and low hearing threshold were reported in mice bearing Dual oxidase 2 (Duox2) gene mutations, which is responsible of oxidation of iodide. Knockout of Pax8 gene in mice resulted in both agenesis of thyroid gland and deafness. Early L-thyroxin therapy prevented the development of deafness in those mice. The expression of thyroid receptor α (TRα) in the external and internal cholera hairs in mice indicates that the thyroid hormones have an important role in the development of the internal ear.